Molecular simulation reveals how the host thromboinflammatory C-type lectin receptor CLEC2 interacts with the receptor-binding domain of SARS-CoV-2
Abstract
Recent studies highlight the pivotal role of a type II transmembrane spleen tyrosine kinase-coupled C-type lectin as a novel pattern recognition host-cell receptor (CLEC2) in driving intense proinflammatory responses through platelet hyperactivation and neutrophil extracellular trap (NET) aggregation upon binding with the SARS-CoV-2 spike protein receptor-binding domain (RBD) in Covid-19 patients. Although direct interactions between the viral RBD and host CLEC2 have been implicated in vascular immunothrombosis, their precise molecular mechanisms remain poorly understood. To bridge this gap, herein, we employed an integrated computational strategy combining physics-based and machine-learning guided three state-of-the-art protein–protein docking tools with classical molecular dynamics simulations at the µ-second time scale to uncover the potential mode of molecular recognition. Our findings, further reinforced by alanine scanning and binding free energy analyses, reveal that both canonical and noncanonical CLEC2 residues, notably Asn120 and Lys190, are critical for recognizing the RBD residues Glu484 and Phe490 within the receptor-binding motif (RBM), which computationally resembles aspects of podoplanin-CLEC2 engagement and presents a plausible hypothesis for how CLEC2 might participate in aggregated NET formation in COVID-19 patients. Steered molecular dynamics simulations further demonstrate the mechanical robustness of these interactions, with the HADDOCK-derived complex exhibiting a superior rupture force compared to the ClusPro-derived complex. These insights suggest the existence of multiple binding modes governing CLEC2–RBD interactions. The outcomes of our study highlight the molecular basis of CLEC2-mediated thromboinflammation in COVID-19, which is driven by the release of extracellular vesicles, and provide a framework for developing targeted therapeutics to mitigate the risk of post-acute Covid-19 sequelae.